# Chromosome evolution and rapid Y chromosome degeneration

> **NIH NIH R35** · TRUSTEES OF INDIANA UNIVERSITY · 2024 · $388,319

## Abstract

PROJECT SUMMARY
Chromosomes are a fundamental structure necessary for the faithful transmission of genetic
information. At the center of chromosome formation and segregation are centromeres, whose
underlying DNA sequence often make up a surprisingly large portion of a genome. Often
composed of repetitive satellite sequences, they are found to evolve and change quickly across
species, likely due to selfish behavior. Along with centromeric changes in sequence and position,
one of the most dramatic genomic changes that can occur is when a chromosome becomes
involved in sex determination. Over time, sex chromosomes typically diverge dramatically in gene
content, gene expression, transposable element content, and levels of genetic variation. These
types of chromosomal changes can be the root of a surprising amount of variation, and we still
have a poor understanding of how and why these changes occur. The proposed research is a
comprehensive examination of chromosome evolution and genome structure in Drosophila, one
of the most powerful and heavily studied systems in genetics. Using chromosome-scale genome
assemblies coupled with genomics and bioinformatics-based approaches, this research will
identify rapidly evolving centromeric satellite sequences across the group to better understand
the tempo of satellite turnover and potential role in karyotypic changes. Additionally, comparative
analyses will for the first time systematically identify genus-wide chromosome evolution and
constraints on gene order and organization. The unique features of Drosophila – numerous
species, small genomes, few chromosomes, ease of karyotyping – make a large-scale
comparative analysis tracking the fates of centromeric satellite sequence and chromosome arms
possible. The proposed research will also investigate a system with very young sex chromosomes
where multiple Y types that vary in their gene content are likely responsible for the evolution of
reproductive incompatibilities between populations. The proposed research will use a
combination of whole genome sequencing and assembly of multiple divergent Y chromosomes,
functional characterization of the diverging X and Y, and population genomic analyses, to link Y
degeneration with restricted gene flow in natural populations. Together, these projects will take
advantage of the unique attributes of two systems to understand the processes that lead to major
changes in karyotype, and variation in degeneration and gene regulation of young sex
chromosomes. More broadly, this research will provide a deeper understanding of the
maintenance of, and variation in, chromosome structure and function that we see across the tree
of life.

## Key facts

- **NIH application ID:** 10891551
- **Project number:** 5R35GM151123-02
- **Recipient organization:** TRUSTEES OF INDIANA UNIVERSITY
- **Principal Investigator:** Ryan Bracewell
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $388,319
- **Award type:** 5
- **Project period:** 2023-08-01 → 2028-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10891551

## Citation

> US National Institutes of Health, RePORTER application 10891551, Chromosome evolution and rapid Y chromosome degeneration (5R35GM151123-02). Retrieved via AI Analytics 2026-06-01 from https://api.ai-analytics.org/grant/nih/10891551. Licensed CC0.

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